tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

new vmd shell to prepare vmd runs

Browse Source
This commit is contained in:
araven
2017-11-17 09:31:09 +01:00
committed by julient31
parent 813343928a
commit 1828274a99
2 changed files with 91 additions and 158 deletions
Download Patch File Download Diff File Expand all files Collapse all files

170
examples/SPIN/vmd_nano.vmd → examples/SPIN/prepare_vmd.sh Normal file → Executable file
View File

@ -1,79 +1,91 @@
proc vmd_draw_arrow {mol start end} {
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.05
graphics $mol cone $middle $end radius 0.01 color 3
}
proc vmd_draw_vector {args} {
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
# defaults
set scale 3.0
set res 5
set radius 0.1
set filled yes
if {[llength $args] < 3} {
error "wrong # args: should be $usage"
}
set mol [lindex $args 0]
set center [lindex $args 1]
set vector [lindex $args 2]
if {[llength $center] != 3 || [llength $vector] != 3} {
error "wrong type of args: should be $usage"
}
foreach {flag value} [lrange $args 3 end] {
switch -glob $flag {
scale {set scale $value}
res* {set res $value}
rad* {set radius $value}
fill* {set filled $value}
default {error "unknown option '$flag': should be $usage" }
}
}
set vechalf [vecscale [expr $scale * 0.5] $vector]
return [list \
[graphics $mol color yellow]\
[graphics $mol cylinder [vecsub $center $vechalf]\
[vecadd $center [vecscale 0.7 $vechalf]] \
radius $radius resolution $res filled $filled] \
[graphics $mol color orange]\
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
resolution $res]]
}
proc vmd_draw_spin {args} {
global molid
graphics $molid delete all
set frame [molinfo $molid get frame]
set natoms [molinfo $molid get numatoms]
for {set i 0} {$i < $natoms} {incr i} {
set sel [atomselect top "index $i"]
# set sel [atomselect top "index 1200"]
set coords [lindex [$sel get {x y z}] $molid]
set velocities [lindex [$sel get {vx vy vz}] $molid]
draw vector $coords $velocities
set uvx [lindex [$sel get {vx}] $molid]
set uvy [lindex [$sel get {vy}] $molid]
set uvz [lindex [$sel get {vz}] $molid]
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
$sel set user $uvy
#draw vector $coords {0.0 uvy 0.0}
}
#pbc box -color 3
}
proc enable_trace {} {
global vmd_frame
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
}
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump_spin_T100.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
scale by 0.5
animate style Loop
enable_trace
#!/bin/bash
# example prepare_vmd.sh /home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj
# you will get a return file
echo "vmd script for file $1 is preparing..."
timestamp(){
date +%s
}
TS=$(timestamp)
FILE=view_${TS}.vmd
cat >${FILE} <<EOF
proc vmd_draw_arrow {mol start end} {
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.05
graphics $mol cone $middle $end radius 0.01 color 3
}
proc vmd_draw_vector {args} {
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
# defaults
set scale 3.0
set res 5
set radius 0.1
set filled yes
if {[llength $args] < 3} {
error "wrong # args: should be $usage"
}
set mol [lindex $args 0]
set center [lindex $args 1]
set vector [lindex $args 2]
if {[llength $center] != 3 || [llength $vector] != 3} {
error "wrong type of args: should be $usage"
}
foreach {flag value} [lrange $args 3 end] {
switch -glob $flag {
scale {set scale $value}
res* {set res $value}
rad* {set radius $value}
fill* {set filled $value}
default {error "unknown option '$flag': should be $usage" }
}
}
set vechalf [vecscale [expr $scale * 0.5] $vector]
return [list \
[graphics $mol color yellow]\
[graphics $mol cylinder [vecsub $center $vechalf]\
[vecadd $center [vecscale 0.7 $vechalf]] \
radius $radius resolution $res filled $filled] \
[graphics $mol color orange]\
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
resolution $res]]
}
proc vmd_draw_spin {args} {
global molid
graphics $molid delete all
set frame [molinfo $molid get frame]
set natoms [molinfo $molid get numatoms]
for {set i 0} {$i < $natoms} {incr i} {
set sel [atomselect top "index $i"]
set coords [lindex [$sel get {x y z}] $molid]
set velocities [lindex [$sel get {vx vy vz}] $molid]
draw vector $coords $velocities
set uvx [lindex [$sel get {vx}] $molid]
set uvy [lindex [$sel get {vy}] $molid]
set uvz [lindex [$sel get {vz}] $molid]
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
$sel set user $uvy
#draw vector $coords {0.0 uvy 0.0}
}
#pbc box -color 3
}
proc enable_trace {} {
global vmd_frame
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
}
set molid [mol addfile {$1} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
scale by 0.5
animate style Loop
enable_trace
EOF
echo "$FILE is ready..."

79
examples/SPIN/vmd_nano_2.vmd
View File

@ -1,79 +0,0 @@
proc vmd_draw_arrow {mol start end} {
set middle [vecadd $start [vecscale 0.9 [vecsub $end $start]]]
graphics $mol cylinder $start $middle radius 0.05
graphics $mol cone $middle $end radius 0.01 color 3
}
proc vmd_draw_vector {args} {
set usage {"draw vector {x1 y1 z1} {x2 y2 z2} [scale <s>] [resolution <res>] [radius <r>] [filled <yes/no>]"}
# defaults
set scale 3.0
set res 5
set radius 0.1
set filled yes
if {[llength $args] < 3} {
error "wrong # args: should be $usage"
}
set mol [lindex $args 0]
set center [lindex $args 1]
set vector [lindex $args 2]
if {[llength $center] != 3 || [llength $vector] != 3} {
error "wrong type of args: should be $usage"
}
foreach {flag value} [lrange $args 3 end] {
switch -glob $flag {
scale {set scale $value}
res* {set res $value}
rad* {set radius $value}
fill* {set filled $value}
default {error "unknown option '$flag': should be $usage" }
}
}
set vechalf [vecscale [expr $scale * 0.5] $vector]
return [list \
[graphics $mol color yellow]\
[graphics $mol cylinder [vecsub $center $vechalf]\
[vecadd $center [vecscale 0.7 $vechalf]] \
radius $radius resolution $res filled $filled] \
[graphics $mol color orange]\
[graphics $mol cone [vecadd $center [vecscale 0.6 $vechalf]] \
[vecadd $center $vechalf] radius [expr $radius * 2.5] \
resolution $res]]
}
proc vmd_draw_spin {args} {
global molid
graphics $molid delete all
set frame [molinfo $molid get frame]
set natoms [molinfo $molid get numatoms]
for {set i 0} {$i < $natoms} {incr i} {
set sel [atomselect top "index $i"]
# set sel [atomselect top "index 1200"]
set coords [lindex [$sel get {x y z}] $molid]
set velocities [lindex [$sel get {vx vy vz}] $molid]
draw vector $coords $velocities
set uvx [lindex [$sel get {vx}] $molid]
set uvy [lindex [$sel get {vy}] $molid]
set uvz [lindex [$sel get {vz}] $molid]
$sel set user [vecadd [vecadd [vecscale $uvy $uvy] [vecscale $uvz $uvz] ] [vecscale $uvx $uvx]]
$sel set user $uvy
#draw vector $coords {0.0 uvy 0.0}
}
#pbc box -color 3
}
proc enable_trace {} {
global vmd_frame
trace variable vmd_frame([molinfo top]) w vmd_draw_spin
}
set molid [mol addfile {/home/jtranch/Documents/lammps/src/dump_VSRSV.lammpstrj} type {lammpstrj} autobonds off first 0 last -1 step 1 waitfor all]
scale by 0.5
animate style Loop
enable_trace